+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-FE-ND-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
Created a new atom named: O01 within residue: .R<HEM 187>
Created a new atom named: O02 within residue: .R<HEM 187>
ERROR: Comparing atoms
.R<HEM 187>.A<ND 55>,
.R<HEM 187>.A<NC 39>,
.R<HEM 187>.A<NB 23>, and
.R<HEM 187>.A<NA 2>
to atoms
.R<HEM 187>.A<ND 55>,
.R<HEM 187>.A<NC 39>,
.R<HEM 187>.A<O1 74>, and
.R<HEM 187>.A<NA 2>
This error may be due to faulty Connection atoms.
!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 142
!FATAL: Message: Atom named O1 from HEM did not match !
!
!ABORTING.
On Sun, Jul 2, 2017 at 11:57 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:
> Hi everyone
> I am trying to load pdb file that consist of heme---O2 through xleap i
> use these commands
> source leaprc.protein.ff14SB
> source leaprc.gaff
> loadamberparams argn.frcmod
> loadamberprep argn.in
> loadpdb oxyhem.pdb
>
> xleap close
> and these error show on terminal window after closing xleap
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-NC-FE-*
> +--- With Sp2 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> +Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
> +---Tried to superimpose torsions for: *-FE-ND-*
> +--- With Sp0 - Sp0
> +--- Sp0 probably means a new atom type is involved
> +--- which needs to be added via addAtomTypes
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named O1 from HEM did not match !
> !
> !ABORTING.
>
>
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Received on Sun Jul 02 2017 - 21:30:02 PDT
